The soil organic carbon (SOC) saturation deficit (Csd) of silt and clay fractions represents the potential for SOC sequestration in a stable form and can influence organic C stabilization efficiency. Little is known, however, about temporal changes of stable soil Csd and how it is affected by soil properties, climate and C inputs. We investigated the temporal changes in the Csd of fine fractions (<53 μm) and examined the factors controlling these changes at three dry-land sites with 17-year fertilizer management histories in China. The rates of change in the stable soil Csd under manure treatments varied from -0.72 to -1.24% yr-1 after 17 years of fertilization, indicating that stable C levels under manure treatments were significantly higher than those under other treatments. Stable soil Csd was controlled by a combination of soil properties, temperature, and C inputs at all sites, and the higher variance of Csd of fine fractions can be explained by the soil properties (up to 50%). Furthermore, the quantity of C inputs was the most influential variable for stable soil Csd. These results revealed key controls on stable C sequestration potential and indicated the need to develop management strategies to promote stable C sequestration under long-term intensive fertilization.